Citation: Min Guo, Kai Zhao, Xingwen Peng, Xiangyang He, Jin Deng, Bo Wang, Xinglou Yang, Libiao Zhang. Pangolin HKU4-related coronaviruses found in greater bamboo bats from southern China .VIROLOGICA SINICA, 2023, 38(6) : 868-876.  http://dx.doi.org/10.1016/j.virs.2023.11.003

Pangolin HKU4-related coronaviruses found in greater bamboo bats from southern China

  • Coronavirus (CoV) spillover originating from game animals, particularly pangolins, is currently a significant concern. Meanwhile, vigilance is urgently needed for coronaviruses carried by bats, which are known as natural reservoirs of many coronaviruses. In this study, we collected 729 anal swabs of 20 different bat species from nine locations in Yunnan and Guangdong provinces, southern China, in 2016 and 2017, and described the molecular characteristics and genetic diversity of alphacoronaviruses (αCoVs) and betacoronaviruses (βCoVs) found in these bats. Using RT-PCR, we identified 58 (8.0%) bat CoVs in nine bat species from six locations. Furthermore, using the Illumina platform, we obtained two representative full-length genomes of the bat CoVs, namely TyRo-CoV-162275 and TyRo-CoV-162269. Sequence analysis showed that TyRo-CoV-162275 shared the highest identity with Malayan pangolin (Manis javanica) HKU4-related coronaviruses (MjHKU4r-CoVs) from Guangxi Province, whereas TyRo-CoV-162269 was closely related to HKU33-CoV discovered in a greater bamboo bat (Tylonycteris robustula) from Guizhou Province. Notably, TyRo-CoV-162275 has a putative furin protease cleavage site in its S protein and is likely to utilize human dipeptidyl peptidase-4 (hDPP4) as a cell-entry receptor, similar to MERS-CoV. To the best of our knowledge, this is the first report of a bat HKU4r-CoV strain containing a furin protease cleavage site. These findings expand our understanding of coronavirus geographic and host distributions.

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    1. Carrington, C.V., Foster, J.E., Zhu, H.C., Zhang, J.X., Smith, G.J., Thompson, N., Auguste, A.J., Ramkissoon, V., Adesiyun, A.A., Guan, Y., 2008. Detection and phylogenetic analysis of group 1 coronaviruses in South American bats. Emerg.Infect. Dis. 14, 1890–1893.

    2. Chen, J., Yang, X., Si, H., Gong, Q., Que, T., Li, J., Li, Y., Wu, C., Zhang, W., Chen, Y., Luo, Y., Zhu, Y., Li, B., Luo, D., Hu, B., Lin, H., Jiang, R., Jiang, T., Li, Q., Liu, M., Xie, S., Su, J., Zheng, X., Li, A., Yao, Y., Yang, Y., Chen, P., Wu, A., He, M., Lin, X., Tong, Y., Hu, Y., Shi, Z.L., Zhou, P., 2023. A bat MERS-like coronavirus circulates in pangolins and utilizes human DPP4 and host proteases for cell entry. Cell 186, 850–863.e816.

    3. Cui, J., Li, F., Shi, Z.L., 2019. Origin and evolution of pathogenic coronaviruses. Nat. Rev.Microbiol. 17, 181–192.

    4. Drexler, J.F., Gloza-Rausch, F., Glende, J., Corman, V.M., Muth, D., Goettsche, M., Seebens, A., Niedrig, M., Pfefferle, S., Yordanov, S., Zhelyazkov, L., Hermanns, U., Vallo, P., Lukashev, A., Müller, M.A., Deng, H., Herrler, G., Drosten, C., 2010.Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences. J. Virol. 84, 11336–11349.

    5. Fan, Y., Zhao, K., Shi, Z.L., Zhou, P., 2019. Bat coronaviruses in China. Viruses 11, 210.

    6. He, W.T., Hou, X., Zhao, J., Sun, J., He, H., Si, W., Wang, J., Jiang, Z., Yan, Z., Xing, G., Lu, M., Suchard, M.A., Ji, X., Gong, W., He, B., Li, J., Lemey, P., Guo, D., Tu, C., Holmes, E.C., Shi, M., Su, S., 2022. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell 185, 1117–1129.e1118.

    7. Hu, B., Zeng, L.P., Yang, X.L., Ge, X.Y., Zhang, W., Li, B., Xie, J.Z., Shen, X.R., Zhang, Y.Z., Wang, N., Luo, D.S., Zheng, X.S., Wang, M.N., Daszak, P., Wang, L.F., Cui, J., Shi, Z.L., 2017. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 13, e1006698.

    8. Lam, T.T., Jia, N., Zhang, Y.W., Shum, M.H., Jiang, J.F., Zhu, H.C., Tong, Y.G., Shi, Y.X., Ni, X.B., Liao, Y.S., Li, W.J., Jiang, B.G., Wei, W., Yuan, T.T., Zheng, K., Cui, X.M., Li, J., Pei, G.Q., Qiang, X., Cheung, W.Y., Li, L.F., Sun, F.F., Qin, S., Huang, J.C., Leung, G.M., Holmes, E.C., Hu, Y.L., Guan, Y., Cao, W.C., 2020. Identifying SARSCoV-2-related coronaviruses in Malayan pangolins. Nature 583, 282–285.

    9. Langeland, N., Moore, L.J., 1990. Reduction of HSV-1 binding to BHK cells after treatment with phosphatidylinositol-specific phospholipase C. FEBS Lett. 277, 253–256.

    10. Latinne, A., Hu, B., Olival, K.J., Zhu, G., Zhang, L., Li, H., Chmura, A.A., Field, H.E., Zambrana-Torrelio, C., Epstein, J.H., Li, B., Zhang, W., Wang, L.F., Shi, Z.L., Daszak, P., 2020. Origin and cross-species transmission of bat coronaviruses in China.Nat. Commun. 11, 4235.

    11. Lau, S.K., Woo, P.C., Li, K.S., Huang, Y., Wang, M., Lam, C.S., Xu, H., Guo, R., Chan, K.H., Zheng, B.J., Yuen, K.Y., 2007. Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome. Virology 367, 428–439.

    12. Li, W., Shi, Z., Yu, M., Ren, W., Smith, C., Epstein, J.H., Wang, H., Crameri, G., Hu, Z., Zhang, H., Zhang, J., McEachern, J., Field, H., Daszak, P., Eaton, B.T., Zhang, S., Wang, L.F., 2005. Bats are natural reservoirs of SARS-like coronaviruses. Science 310, 676–679.

    13. Sanchez, C.A., Li, H., Phelps, K.L., Zambrana-Torrelio, C., Wang, L.F., Zhou, P., Shi, Z.L., Olival, K.J., Daszak, P., 2022. A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia. Nat. Commun. 13, 4380.

    14. Shi, W., Shi, M., Que, T.C., Cui, X.M., Ye, R.Z., Xia, L.Y., Hou, X., Zheng, J.J., Jia, N., Xie, X., Wu, W.C., He, M.H., Wang, H.F., Wei, Y.J., Wu, A.Q., Zhang, S.F., Pan, Y.S., Chen, P.Y., Wang, Q., Li, S.S., Zhong, Y.L., Li, Y.J., Tan, L.H., Zhao, L., Jiang, J.F., Hu, Y.L., Cao, W.C., 2022. Trafficked Malayan pangolins contain viral pathogens of humans. Nat Microbiol 7, 1259–1269.

    15. Tang, X.C., Zhang, J.X., Zhang, S.Y., Wang, P., Fan, X.H., Li, L.F., Li, G., Dong, B.Q., Liu, W., Cheung, C.L., Xu, K.M., Song, W.J., Vijaykrishna, D., Poon, L.L., Peiris, J.S., Smith, G.J., Chen, H., Guan, Y., 2006. Prevalence and genetic diversity of coronaviruses in bats from China. J. Virol. 80, 7481–7490.

    16. Wacharapluesadee, S., Duengkae, P., Rodpan, A., Kaewpom, T., Maneeorn, P., Kanchanasaka, B., Yingsakmongkon, S., Sittidetboripat, N., Chareesaen, C., Khlangsap, N., Pidthong, A., Leadprathom, K., Ghai, S., Epstein, J.H., Daszak, P., Olival, K.J., Blair, P.J., Callahan, M.V., Hemachudha, T., 2015. Diversity of coronavirus in bats from Eastern Thailand. Virol. J. 12, 57.

    17. Wang, L., Fu, S., Cao, Y., Zhang, H., Feng, Y., Yang, W., Nie, K., Ma, X., Liang, G., 2017.Discovery and genetic analysis of novel coronaviruses in least horseshoe bats in southwestern China. Emerg Microbes Infect 6, e14.

    18. Wu, Z., Yang, L., Ren, X., Zhang, J., Yang, F., Zhang, S., Jin, Q., 2016. ORF8-related genetic evidence for Chinese horseshoe bats as the source of human severe acute respiratory syndrome coronavirus. J. Infect. Dis. 213, 579–583.

    19. Xiao, K., Zhai, J., Feng, Y., Zhou, N., Zhang, X., Zou, J.J., Li, N., Guo, Y., Li, X., Shen, X., Zhang, Z., Shu, F., Huang, W., Li, Y., Zhang, Z., Chen, R.A., Wu, Y.J., Peng, S.M., Huang, M., Xie, W.J., Cai, Q.H., Hou, F.H., Chen, W., Xiao, L., Shen, Y., 2020. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature 583, 286–289.

    20. Yang, J., Skaro, M., Chen, J., Zhan, D., Lyu, L., Gay, S., Kandeil, A., Ali, M.A., Kayali, G., Stoianova, K., Ji, P., Alabady, M., Bahl, J., Liu, L., Arnold, J., 2023. The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic.Sci. Rep. 13, 5571.

    21. Yang, T., 2016. A revised bat (Mammalia: Chiroptera) checklist for Guizhou, China.Biodivers. Sci. 24, 957–962.

    22. Zaki, A.M., van Boheemen, S., Bestebroer, T.M., Osterhaus, A.D., Fouchier, R.A., 2012.Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N. Engl.J. Med. 367, 1814–1820.

    23. Zhou, P., Fan, H., Lan, T., Yang, X.L., Shi, W.F., Zhang, W., Zhu, Y., Zhang, Y.W., Xie, Q.M., Mani, S., Zheng, X.S., Li, B., Li, J.M., Guo, H., Pei, G.Q., An, X.P., Chen, J.W., Zhou, L., Mai, K.J., Wu, Z.X., Li, D., Anderson, D.E., Zhang, L.B., Li, S.Y., Mi, Z.Q., He, T.T., Cong, F., Guo, P.J., Huang, R., Luo, Y., Liu, X.L., Chen, J., Huang, Y., Sun, Q., Zhang, X.L., Wang, Y.Y., Xing, S.Z., Chen, Y.S., Sun, Y., Li, J., Daszak, P., Wang, L.F., Shi, Z.L., Tong, Y.G., Ma, J.Y., 2018. Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin. Nature 556, 255–258.

    24. Zhou, P., Yang, X.L., Wang, X.G., Hu, B., Zhang, L., Zhang, W., Si, H.R., Zhu, Y., Li, B., Huang, C.L., Chen, H.D., Chen, J., Luo, Y., Guo, H., Jiang, R.D., Liu, M.Q., Chen, Y., Shen, X.R., Wang, X., Zheng, X.S., Zhao, K., Chen, Q.J., Deng, F., Liu, L.L., Yan, B., Zhan, F.X., Wang, Y.Y., Xiao, G.F., Shi, Z.L., 2020. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273.

    25. Zhu, W, Huang, Y, Gong, J, Dong, L, Yu, X, Chen, H, Li, D, Zhou, L, Yang, J, Lu, S, 2023.A novel bat coronavirus with a polybasic furin-like cleavage site. Virol Sin 38, 344–350.

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    Pangolin HKU4-related coronaviruses found in greater bamboo bats from southern China

      Corresponding author: Xinglou Yang, yangxinglou@mail.kiz.ac.cn
      Corresponding author: Libiao Zhang, zhanglb@giz.gd.cn
    • a. Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China;
    • b. Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650023, China;
    • c. Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24060, USA;
    • d. Hubei Jiangxia Lab, Wuhan, 430071, China

    Abstract: Coronavirus (CoV) spillover originating from game animals, particularly pangolins, is currently a significant concern. Meanwhile, vigilance is urgently needed for coronaviruses carried by bats, which are known as natural reservoirs of many coronaviruses. In this study, we collected 729 anal swabs of 20 different bat species from nine locations in Yunnan and Guangdong provinces, southern China, in 2016 and 2017, and described the molecular characteristics and genetic diversity of alphacoronaviruses (αCoVs) and betacoronaviruses (βCoVs) found in these bats. Using RT-PCR, we identified 58 (8.0%) bat CoVs in nine bat species from six locations. Furthermore, using the Illumina platform, we obtained two representative full-length genomes of the bat CoVs, namely TyRo-CoV-162275 and TyRo-CoV-162269. Sequence analysis showed that TyRo-CoV-162275 shared the highest identity with Malayan pangolin (Manis javanica) HKU4-related coronaviruses (MjHKU4r-CoVs) from Guangxi Province, whereas TyRo-CoV-162269 was closely related to HKU33-CoV discovered in a greater bamboo bat (Tylonycteris robustula) from Guizhou Province. Notably, TyRo-CoV-162275 has a putative furin protease cleavage site in its S protein and is likely to utilize human dipeptidyl peptidase-4 (hDPP4) as a cell-entry receptor, similar to MERS-CoV. To the best of our knowledge, this is the first report of a bat HKU4r-CoV strain containing a furin protease cleavage site. These findings expand our understanding of coronavirus geographic and host distributions.

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